See http://madoc.univ-nantes.fr/course/view.php?id=29100 for the whole open courseware.

1. Methodology and Tools for Research:
Future of science
Yannick Prié
Polytech Nantes, University of Nantes
Master DMKM, 2014-2015
CC BY-SA 4.0

2. Attribution-ShareAlike 4.0
International (CC BY-SA 4.0)
• This course "Methodology and Tools for Research: Future of
Science" by Yannick Prié is licensed CC BY-SA 4.0
• This license covers the general organization of the material, the
textual content, the figures, etc. except where indicated.
• This license means that you can share and adapt this course,
provided you give appropriate credit to the author and distribute your
contributions under the same license as the original
◦ for more information about this license, see
http://creativecommons.org/licenses/by-sa/4.0/
• For any comment on this course, do not hesitate to contact me:
yannick.prie@univ-nantes.fr or @yprie

3. Objectives of this course
• Get an idea of the various directions along which
science could evolve in a digital age
• Get basic notions on the open access topic
• Launch the collaborative writing assignment to
go further on several topics
• Ressources for the course
http://www.scoop.it/t/toolsandmethodologyforresearch

4. Outline
• Science in the digital Age
• Open Access
• Assignment

5. Outline
• Science in the digital Age
• Open Access
• Assignment

6. Science occurs in a networked environment
• Based on technologies for
◦ information storage
◦ communication
• History
◦ Written Age à Print Age à Digital Age
The Great Library of Alexandria
by O. Von Corven is Public Domain
Server room at CERN
by Torkild Retvedt is CC-BY SA 2.0
One wing of the Merton College library
by Tom Murphy VIIis CC-BY SA 3.0

7. Digital Age?
• Computers
• Networks
then
• Home network access
• Mobile devices
• Cloud
• Social networks
• Probes everywhere
Deep,
uncontrolled
changes
in society

8. Science processes are affected too
• Funding
• Data collection
• Data processing
• Publications
• Conferences
• Evaluation
• Discussion
• …
Classical processes
that evolve like
in others domains
• e.g. collaboraPve wriPng,
use of skype
New processes made
possible by digital
technology
• e.g. open access

9. Massive use of computers in the labs
• Knowledge management
◦ sharing of references, access to digital libraries
• Personal knowledge management
◦ reference management, annotations
• Publication workflow support
◦ tools for drawing molecules in chemistry
◦ conference workflows, from paper to PDF
• Experimental data management
◦ raw results, experimental settings, results
◦ mining, interactive visualisation
• Simulation
◦ in biology, physics, etc.

10. And then… Science 2.0
• Emergent new practices
◦ Based on information technologies
• Some examples
◦ Managing collaboration and identity
• web 2.0 tools used for science
◦ Open-data and e-science
• collecting, sharing data and processing
◦ Digital humanities
• humanities get digital
◦ Open access
• to publications

11. Blogs,Twitter, wikis and web-based tools
Wordle tag cloud on social compuPng
by Daniel Iversen is CC-BY SA 2.0

12. hypotheses.org (dec 2012)

13. hypotheses.org (dec 2012)

14. Open data and e-science
• Sharing data
◦ Collaborative worldwide efforts
• Human Genome,
Digital Sky Survey (sdss.org)…
◦ Open Data as a technology
◦ Sharing data and code
with article
• E.g. Warming Ocean Threatens Sea Life
◦ Sharing processing
• Grid computing (cloud)
• Opening research data
◦ e.g. funding / projects
information
Enhanced image
of the Milky Way
satellite galaxy Boo I
by Vasily Belokurov
is Public Domain

15. Digital Humanities
• Use of computer tools and techniques to carry out
research work in the humanities
• Multiple examples
◦ Digitization
◦ Collaboration tools / annotations
◦ Text manipulation
• Textual corpora
• Ancient manuscript images
◦ Data aggregation and mining
• Sociological data
◦ Data visualisation
• in Nantes: see graph visualisation of social networks in the middle
age
◦ …

16. Example
David Chavalarias,
Jean-Philippe Cointet.
Phylomeme(c Pa,erns in
Science Evolu(on—The Rise
and Fall of Scien(fic Fields.
PLOS ONE. Feb 2013
Studying scienPfic
concepts rise and
fall.
hYp://www.plosone.org/arPcle/info%3Adoi%2F10.1371%2Fjournal.pone.0054847

17. Citizen science
• Public participation in research
• Not new
◦ crowdsourcing: bird watching,
amateur archaeology, etc.
• New digital era
◦ Access to information
• any data, also medical data
◦ Capacity to collect information
• mobile devices
◦ Capacity to analyse information
• general raise in education
• available tools for analysis (stats, visualisation, etc.)
• Towards extreme citizen science?
◦ oriented towards issues that concern people
Scanning a lake for Common Loons for the
Common Loon Monitoring CiPzen Science
by GlacierNPS is CC-BY SA 2.0

19. The Tao of Open Science for Ecology
hYp://www.esajournals.org/doi/full/10.1890/ES14-00402.1

20. Outline
• Science in the digital Age
• Open Access
• Assignment

21. Access to publications
• Classical model
◦ Scientists write and review papers for journals
◦ Publishers publish papers in journals
◦ Universities pay fees to publishers to provide access
to journals in their libraries
• into which they remain accessible indefinitely
• Worked well for a long time
◦ journal fees were reasonable

22. Digital versions of articles
• No need for paper anymore
◦ instant access, simplicity, no printing cost…
◦ pay per view
• Facilitation of reviewing / editing workflows
• Digital archiving
◦ publishers become librarians

23. Recent years
• Universities
◦ Less and less money
• Publishers
◦ Reasonable ones
• reasonable fees, free access after 5 or 10 years,
◦ Greedy ones
• package selling
◦ buy 200 journals to get access to the 3 that interest you
◦ nationwide “big deals”
• rise of fees with no relation to inflation or production costs
◦ + 4-5% each year between 1986 et 2011
• very expensive
• opacity

24. From
L’édi(on scien(fique : son
modèle, ses scandales.
Dans les coulisses de la
publica(on scien(fique
by Laurence Bianchini
(2011)

25. Some figures
• Scientific, technical and medical edition:
◦ 20.2 B$ (2010 - stm-assoc.org)
• Big players
◦ Elsevier: 2200 journals, 25% of all published articles
◦ Springer: 2000 journals
◦ Wiley-Blackwell: 1500 journal
◦ Nature Publishing Group
• Rentability
◦ 30% profit (2010-2011, The Economist)

26. Others problems
• Authors abandon all of their rights to publishers
• Why would state fund both
◦ the production of an article
◦ and the access to the article ?
à public should be able to access what they pay for
• Long term archival not likely to happen with
private companies
• Corruption in the medical / pharmaceutical
domain
◦ ghost writers (from industry), false journals (Elsevier)

27. Open Access
• Provide the public with unrestricted, free
access to scholarly research—much of which
is publicly funded
◦ Making the research publicly available to everyone, free of
charge and without most copyright and licensing restrictions, will
accelerate scientific research efforts and allow authors to reach a
larger number of readers.
• Budapest Open Access Initiative (2002)
◦ 10 recommendations
• Two main models: Green / Gold
◦ Stevan Harnad & al. The green and the gold roads to Open
Access. Nature Web Focus. http://www.nature.com/nature/focus/
accessdebate/21.html
hYp://www.opensocietyfoundaPons.org/openaccess/
boai-10-recommendaPons

28. Green
• Also called “auto-archiving”
• Researchers deposit a version of their articles on an institutional
archive
◦ worldwide (e.g. arXiv.org)
◦ nationwide (e.g. HAL)
◦ community wide
◦ local (e.g. University)
• The version can be
◦ a preprint
• last accepted version, not the published one
◦ the final version
• with possibly and embargo depending on the publisher’s policy
• Deposit can be mandatory or not
◦ e.g. to get funds associated to a grant, for a publication to be
considered in a lab evaluation, etc.

29. arXiv.org: the ancestor
Physicists,1991 - Preprint archive
Started in August 1991,
arXiv.org (formerly
xxx.lanl.gov) is a highly-
automated electronic archive
and distribution server for
research articles. Covered
areas include physics,
mathematics, computer
science, nonlinear sciences,
quantitative biology and
statistics.
hYp://arxiv.org/ (dec 2013)

30. Gold
• Reading is free
• Several models
◦ Subventions
◦ Fremium
◦ Author / payer: “publication fees”
• “fair gold”
• not so fair gold
◦ Springer 2012: 2000€ per article (personal experience)
◦ Taylor & Francis 2013: 2950€ (twitter march 2013)
• Institutions have to pay
• The model big players prefer and advocate
◦ Elsevier, Springer, etc.

31. Example: PLoS One
• “International, peer-reviewed,
open-access, online publication
• Research from any scientific discipline.
◦ Open-access—freely accessible online, authors retain copyright
◦ Fast publication times
◦ Peer review by expert, practicing researchers
◦ Post-publication tools to indicate quality and impact
◦ Community-based dialogue on articles
◦ Worldwide media coverage”
• Fees
◦ Group A: 0$ / article
◦ Group B: 500$ / article
◦ Others: 1300 to 2900$
Good read :
Goals of science vs Goals of scienPsts
(& a love leYer to PLOS One)

32. Example: eLife
• Life science, biomedicine
◦ open access
◦ no charge to authors (“at least for an initial period”)
◦ no limit to length or additional submitted material
• New model of peer reviewing
◦ reviewers gather electronically to decide the fate of the paper
à better for reaching a consensus
◦ instruction for major revisions are clear
à authors do not have to guess
◦ decision letter and author response are published with the paper
à reader know what happened
◦ if the paper is not accepted, it can be submitted elsewhere
rapidly with the elife reviews
à no loss of expertise

33. Example: f1000research.com
publish first, then evaluate
hYp://f1000research.com/arPcles/2-195/v2

34. Example: peerj.com
Biological and Medical Sciences / cheap Gold OA
hYps://peerj.com/pricing/ (dec 2013)
40% of peer-reviewers name themselves, 80% of
authors reproduce their peer review history.

35. Gold variant: latinum
CLEO - Centre for Open Electronic Publishing
• Between Golf and Green, Freemium model
◦ open access to the text online
◦ supplementary (not too high) pay services
• e.g. getting PDF or epub, download count, etc.
• Prices depend on
◦ Gross Domestic Product of the country
◦ Number of students in humanities + staff
• All income is reinvested in the development of open-
access academic publishing
◦ 2/3 for journals and partner publishers
◦ 1/3 to develop the platform
hYp://www.openediPon.org/8873

36. Gold variant: Diamond
• The reader does not pay for reading
• The author only pays for editing
• The editorial committee owns the journal
• The editor is hired for editing the journal
• The publishing is done by a institional editing
body
• See http://triplec.at/index.php/tripleC/article/view/502/497
Line art drawing of a diamond by
Pearson ScoY Foresman
is Public Domain

37. Hot topic
• 2012: mathematicians community (13000 researchers) threatens to
boycott Elsevier
• 2012: UK announce mandatory gold open access
• 2012 : EU announce open access policy
◦ Gold or Green 6 month – 12 month for social science and humanities
• Feb 2013: US open access policy
◦ “published results of federally funded research freely available to the
public within one year” of publication
• Feb 2013: HAL deposit mandatory for INRIA
• March 2013: Humanities Journals in France want to reject EU 12
month embargo, Counter-petition #iloveopenaccess
• March 2013 : “#btpdf2 #scholrev: Planning the scholarly revolution”
• 2013: episciences.org french platform for peer reviewing + deposit in
arXiv or HAL

38. Hot topic, cont.
• Aug 2013: Swizz Research Fund authorizes project fundung for Gold OA
publishing
◦ not enough money to pay all
• Aug 2013: Italy supports green open access
• Aug 2013: Open Access support wikipedia
◦ availability of papers entails better wk articles
• Fall 2013: UK open-access route too costly, report says (Nature)
• Oct 2013: Nature publishes a paper on fooling gold OA journals
◦ can appear as a piece against OA in general
• Dec 2013: Argentina makes OA deposit mandatory
• End of 2013: hard negociation between French Libraries and Elsevier
• Dec 2013 : Elsevier launches takedown notices on Academia, personal
sites, etc.
• …

39. 2014: the Battle continues
• "11 years after the Berlin Declaration on Open Access,
however, the rise of Open Access appears to inflict little
or no damage on the leading subscription
publishers. » (financial analysist
http://www.richardpoynder.co.uk/Aspesi.pdf)
• Nature papers get « open » (free to read on a dedicated
reader, beggar’s acces (
http://www.computerworlduk.com/blogs/open-enterprise/
open-access-3589444/ )
• Notion of Review on demand, cf.
http://www.epistemio.com/rod
• An mainstrem journal article on french Elsevier deal
raises awareness on Open Access in France

40. One model to rule them all?
• Many disciplines, many different ways of apprehending
things
• There is room for many different models
◦ gold, green, platinum OA + institutional deposit policies
• Computer science: quite conservative
◦ importance of conferences (ACM, IEEE)
• ACM relaxed (a little) its copyright policy in 2013
◦ journals (Elsevier, Springer)
• Gold, expensive OA
◦ may change very fast

41. An article that may be interesting or not, only
185 people may know…
hYp://www.tandfonline.com/doi/abs/
10.1080/01972243.2012.757263#.Uqb0LI08r5Y
(dec 2013)

42. Towards an evolution of reviewing?
Study
IntroducPon
Methods
Results
Conclusion
PublicaPon
Current system
PEER
REVIEW
Study
IntroducPon
Methods
Results
Conclusion
PublicaPon
PEER
REVIEW
(secondary
review)
Study
Results
Conclusion
PublicaPon
PEER
REVIEW
IntroducPon
Methods
(secondary
review)
Two-step review Peer pre-review
(from A New Kind of Peer Review? by NeuroskepPc, 2013)

43. Get Credit for Peer
Review (Publons)
record, showcase, and
verify all your peer review
activity … use your offical
reviewer record in
promotion and funding
applications.
• Easily record and
control verified reviews
• Showcase reviews for
promotion and funding
applications
• Discuss papers post
publication and get
credit

44. The Research Ideas and Outcomes journal publishes all outputs of the research cycle, including: project
proposals, data, methods, workflows, software, project reports and research articles together on a single
collaborative platform, with the most transparent, open and public peer-review process. Our scope
encompasses all areas of academic research, including science, technology, humanities and the social sciences.
hYp://riojournal.com/

45. Outline
• Science in the digital Age
• Open Access
• Assignment: article writing